@Bradyhancock > If you want to use a Sample Deck with only 2 CDJ-2000's, I believe you would have to assign one of the players to a specific Sample Deck and have it only control the samples. The best bet would be to pick up something like a X1 controller just to control your Sample Decks. That would be much easier in my opinion.
When you say you want to use some basic effects with Traktor, what hardware did you want to control the effect with? Your DJM-900?